Long-range restriction mapping

Abstract

Abstract Mapping large and complex genomes relies on techniques that permit the analysis and manipulation of long stretches of DNA, hundreds to thousands of kilobases in length. This has been achieved largely through the developments of pulsed field gel electrophoresis (PFGE)-allowing the resolution of large DNA fragments, and yeast artificial chromosome vectors (YACs) for cloning large DNA fragments. Being able to resolve very large fragments of DNA also necessitates being able to restrict DNA into suitably long length . This can be accomplished with restriction enzymes with large, and therefore rare recognition sequences. In vertebrates, large restriction fragments can also be generated using restriction enzymes with CpG dinucleotides in their recognition sequences (this also applies to plant DNAs and includes enzymes with CpXpGs in their recognition sites). The principle cleavage sites for CpG recognizing enzymes in vertebrate genomic DNA, as well as providing convenient landmarks for the construction of long-range restriction maps, also mark out the position of many of the genes-critically important in organism where only a few per cent of the DNA has a coding capacity. This chapter aims to demonstrate how to create and interpret long-range restriction maps. primarily, of mammalian genomes.